name: ivar_variants
description: Call variants from a BAM file using iVar
keywords:
  - amplicon sequencing
  - variants
  - fasta
tools:
  - ivar:
      description: |
        iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
      homepage: https://github.com/andersen-lab/ivar
      documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
      licence: ["GPL-3.0-or-later"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file
      pattern: "*.bam"
  - fasta:
      type: file
      description: The reference sequence used for mapping and generating the BAM file
      pattern: "*.fa"
  - fai:
      type: file
      description: The index for the reference sequence used for mapping and generating the BAM file
      pattern: "*.fai"
  - gff:
      type: file
      description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
      patter: "*.gff"
  - save_mpileup:
      type: boolean
      description: Save mpileup file generated by ivar variants
      patter: "*.mpileup"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - tsv:
      type: file
      description: iVar generated TSV file with the variants
      pattern: "*.tsv"
  - mpileup:
      type: file
      description: mpileup output from samtools mpileup [OPTIONAL]
      pattern: "*.mpileup"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@andersgs"
  - "@drpatelh"